5WN3

APE1 F266A exonuclease substrate complex with a C/T mismatch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.

Whitaker, A.M.Flynn, T.S.Freudenthal, B.D.

(2018) Nat Commun 9: 399-399

  • DOI: 10.1038/s41467-017-02175-y
  • Primary Citation of Related Structures:  
    5WN0, 5WN1, 5WN2, 5WN3, 5WN4, 5WN5

  • PubMed Abstract: 
  • Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is an essential DNA repair enzyme which uses a single active site to process DNA damage via two distinct activities: (1) AP-endonuclease and (2) 3' to 5' exonuclease. The AP-endonuclease activity cleaves at AP-sites, while the exonuclease activity excises bulkier 3' mismatches and DNA damage to generate clean DNA ends suitable for downstream repair ...

    Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is an essential DNA repair enzyme which uses a single active site to process DNA damage via two distinct activities: (1) AP-endonuclease and (2) 3' to 5' exonuclease. The AP-endonuclease activity cleaves at AP-sites, while the exonuclease activity excises bulkier 3' mismatches and DNA damage to generate clean DNA ends suitable for downstream repair. Molecular details of the exonuclease reaction and how one active site can accommodate various toxic DNA repair intermediates remains elusive despite being biologically important. Here, we report multiple high-resolution APE1-DNA structural snapshots revealing how APE1 removes 3' mismatches and DNA damage by placing the 3' group within the intra-helical DNA cavity via a non-base flipping mechanism. This process is facilitated by a DNA nick, instability of a mismatched/damaged base, and bending of the DNA. These results illustrate how APE1 cleanses DNA dirty-ends to generate suitable substrates for downstream repair enzymes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA. bfreudenthal@kumc.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) lyaseD [auth A], E [auth B]276Homo sapiensMutation(s): 2 
Gene Names: APEX1APEAPE1APEXAPXHAP1REF1
EC: 3.1 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P27695 (Homo sapiens)
Explore P27695 
Go to UniProtKB:  P27695
PHAROS:  P27695
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')A [auth C]11synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DV3))-3')B [auth D]10synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Find similar nucleic acids by:  (by identity cutoff)  |  Structure
      Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')C [auth E]21synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.00 Å
      • R-Value Free: 0.258 
      • R-Value Work: 0.210 
      • R-Value Observed: 0.211 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 71.144α = 90
      b = 65.545β = 110.08
      c = 91.441γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data collection
      HKL-2000data scaling
      PDB_EXTRACTdata extraction
      PHENIXphasing
      HKL-2000data reduction

      Structure Validation

      View Full Validation Report




      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES024431

      Revision History  (Full details and data files)

      • Version 1.0: 2018-02-28
        Type: Initial release
      • Version 1.1: 2019-02-20
        Changes: Author supporting evidence, Data collection
      • Version 1.2: 2019-11-27
        Changes: Author supporting evidence